Integration branch

.circleci/config.yml

@@ -40,9 +40,9 @@ commands:
       - run:
           name: Create Conda Environment
           command: |
-            conda create -v --quiet --prefix << parameters.condaenv >> --show-channel-urls --channel conda-forge "<< parameters.python >>" << parameters.packages >> gmsh
+            mamba create -v --quiet --prefix << parameters.condaenv >> --show-channel-urls --channel conda-forge "<< parameters.python >>" << parameters.packages >>
             source activate ~/project/<< parameters.condaenv >>
-            conda remove --quiet --channel conda-forge --force fipy
+            mamba remove --quiet --channel conda-forge --force fipy
             pip install scikit-fmm
 
   test_fipy:
@@ -87,7 +87,8 @@ commands:
             if [[ ! -z "${FIPY_INLINE}" ]]; then
               << parameters.mpirun >> python setup.py test > /dev/null 2>&1 || true;
             fi
-            << parameters.mpirun >> python setup.py test --deprecation-errors
+            python setup.py develop
+            << parameters.mpirun >> python examples/phase/test.py
 
       - store_artifacts:
           path: test-reports
@@ -147,7 +148,7 @@ commands:
           paths:
             - /opt/conda
             - /root/.cache/pip
-          key: v13-dependencies-{{ arch }}-<< parameters.condaenv >>
+          key: v14-dependencies-{{ arch }}-<< parameters.condaenv >>
 
   restore_conda_cache:
     description: "Restore cache holding conda and pip"
@@ -160,9 +161,9 @@ commands:
     steps:
       - restore_cache:
           keys:
-          - v13-dependencies-{{ arch }}-<< parameters.condaenv >>
+          - v14-dependencies-{{ arch }}-<< parameters.condaenv >>
           # fallback to using the latest cache if no exact match is found
-          - v13-dependencies-
+          - v14-dependencies-
 
   install_dependencies:
     steps:
@@ -173,6 +174,7 @@ commands:
             apt-get --yes install build-essential
             conda config --set always_yes yes --set changeps1 no
             conda config --remove channels defaults
+            conda install --channel conda-forge mamba
 
   remove_extracted_conda_packages:
     description: "force conda to download packages into the cache and then
@@ -248,7 +250,7 @@ jobs:
     steps:
       - install_conda_packages:
           python:   "python=2.7"
-          packages: "fipy \"traitsui<7.0.0\""
+          packages: "fipy \"traitsui<7.0.0\" \"gmsh<4.0\""
           condaenv: "test-environment-27"
 
   conda3_env:
@@ -257,7 +259,7 @@ jobs:
     steps:
       - install_conda_packages:
           python:   "python=3"
-          packages: "fipy pytrilinos"
+          packages: "fipy pytrilinos gmsh"
           condaenv: "test-environment-36"
 
   pip_env:
@@ -433,7 +435,7 @@ jobs:
           name: Lint
           command: |
             source activate ~/project/<< parameters.condaenv >>
-            conda install --channel conda-forge black
+            mamba install --channel conda-forge black
             black --target-version py27 --fast --diff --check setup.py
 
   pyspelling:
@@ -457,7 +459,7 @@ jobs:
           name: Spell Check
           command: |
             source activate ~/project/<< parameters.condaenv >>
-            conda install --channel conda-forge hunspell
+            mamba install --channel conda-forge hunspell
             pip install pyspelling
             wget -O en_US.aff  https://cgit.freedesktop.org/libreoffice/dictionaries/plain/en/en_US.aff?id=a4473e06b56bfe35187e302754f6baaa8d75e54f
             wget -O en_US.dic https://cgit.freedesktop.org/libreoffice/dictionaries/plain/en/en_US.dic?id=a4473e06b56bfe35187e302754f6baaa8d75e54f
@@ -488,10 +490,10 @@ jobs:
           name: install sphinx
           command: |
             source activate ~/project/<< parameters.condaenv >>
-            conda install --channel conda-forge sphinx future
+            mamba install --channel conda-forge sphinx future
             pip install 'sphinxcontrib-bibtex<=0.4.2'
             pip install numpydoc
-            conda install --channel conda-forge matplotlib pandas imagemagick
+            mamba install --channel conda-forge matplotlib pandas imagemagick
 
       - build_html_docs:
           condaenv: << parameters.condaenv >>
@@ -521,10 +523,10 @@ jobs:
           name: install sphinx
           command: |
             source activate ~/project/<< parameters.condaenv >>
-            conda install --channel conda-forge sphinx future
+            mamba install --channel conda-forge sphinx future
             pip install sphinxcontrib-bibtex
             pip install numpydoc
-            conda install --channel conda-forge matplotlib pandas imagemagick
+            mamba install --channel conda-forge matplotlib pandas imagemagick
 
       - run:
           name: Install LaTeX
@@ -592,75 +594,76 @@ jobs:
           path: ~/project/dist
 
 
+
 workflows:
   version: 2
 
   test:
     jobs:
       - conda2_env
       - conda3_env
-#       - build-27-docs:
+# #       - build-27-docs:
+# #           requires:
+# #             - conda2_env
+#       - pip_env
+#       - build-36-docs:
+#           requires:
+#             - conda3_env
+#       - pylint:
 #           requires:
 #             - conda2_env
-      - pip_env
-      - build-36-docs:
-          requires:
-            - conda3_env
-      - pylint:
-          requires:
-            - conda2_env
-      - flake8:
-          requires:
-            - conda2_env
-      - black:
-          requires:
-            - conda3_env
-      - pyspelling:
-          requires:
-            - conda3_env
-      - test-27-pysparse:
-          requires:
-            - conda2_env
-#       - test-27-inline:
+#       - flake8:
 #           requires:
 #             - conda2_env
-#       - test-27-scipy:
+#       - black:
+#           requires:
+#             - conda3_env
+#       - pyspelling:
+#           requires:
+#             - conda3_env
+#       - test-27-pysparse:
 #           requires:
 #             - conda2_env
-      - test-27-petsc-serial:
-          requires:
-            - conda2_env
-      - test-27-petsc-parallel:
+# #       - test-27-inline:
+# #           requires:
+# #             - conda2_env
+      - test-27-scipy:
           requires:
             - conda2_env
+#       - test-27-petsc-serial:
+#           requires:
+#             - conda2_env
+#       - test-27-petsc-parallel:
+#           requires:
+#             - conda2_env
       - test-36-scipy:
           requires:
             - conda3_env
-      - test-36-trilinos-serial:
-          requires:
-            - conda3_env
-      - test-36-trilinos-parallel:
-          requires:
-            - conda3_env
+#       - test-36-trilinos-serial:
+#           requires:
+#             - conda3_env
+#       - test-36-trilinos-parallel:
+#           requires:
+#             - conda3_env
       - test-36-petsc-serial:
           requires:
             - conda3_env
-      - test-36-petsc-parallel:
-          requires:
-            - conda3_env
-      - build-binaries:
-          requires:
-            - conda3_env
-#             - build-36-docs
-#             - pylint
-#             - flake8
-#             - black
-#             - pyspelling
-#             - test-27-pysparse
-#             - test-27-trilinos-serial
-#             - test-27-trilinos-parallel
-#             - test-27-petsc-serial
-#             - test-27-petsc-parallel
-#             - test-36-scipy
-#             - test-36-petsc-serial
-#             - test-36-petsc-parallel
+#       - test-36-petsc-parallel:
+#           requires:
+#             - conda3_env
+#       - build-binaries:
+#           requires:
+#             - conda3_env
+# #             - build-36-docs
+# #             - pylint
+# #             - flake8
+# #             - black
+# #             - pyspelling
+# #             - test-27-pysparse
+# #             - test-27-trilinos-serial
+# #             - test-27-trilinos-parallel
+# #             - test-27-petsc-serial
+# #             - test-27-petsc-parallel
+# #             - test-36-scipy
+# #             - test-36-petsc-serial
+# #             - test-36-petsc-parallel

.travis.yml

@@ -45,11 +45,14 @@ before_install:
   - hash -r
   - conda config --set always_yes yes --set changeps1 no
   - conda update -q conda
-  - conda create --quiet --name test-environment --show-channel-urls --channel conda-forge python=$TRAVIS_PYTHON_VERSION fipy gmsh pytrilinos;
+  - conda install --channel conda-forge mamba
+  - mamba create --quiet --name test-environment --show-channel-urls --channel conda-forge python=$TRAVIS_PYTHON_VERSION fipy pytrilinos;
   - source activate test-environment
-  - conda remove --quiet --channel conda-forge --force fipy
+  - mamba remove --quiet --channel conda-forge --force fipy
   - if [[ $PY3K -eq 0 ]]; then
-      conda install --channel conda-forge "traitsui<7.0.0";
+      mamba install --channel conda-forge "traitsui<7.0.0" "gmsh<4.0";
+    else
+      mamba install --channel conda-forge gmsh;
     fi
   # Useful for debugging any issues with conda
   - conda info -a

INSTALLATION.rst

@@ -118,6 +118,15 @@ Recommended Method
 
 * move on to :ref:`USAGE`.
 
+  .. note::
+
+     conda_ can be
+     `quite <https://www.anaconda.com/blog/understanding-and-improving-condas-performance>`_
+     `slow <https://medium.com/@marius.v.niekerk/conda-metachannel-f962241c9437>`_
+     to resolve all dependencies when performing
+     an installation.  You may wish to consider using the alternative
+     mamba_ installation manager to speed things up.
+
   .. note::
 
      On Linux_ and `Mac OS X`_, you should have a pretty complete system
@@ -141,6 +150,7 @@ Recommended Method
 .. _Windows: http://www.microsoft.com/windows/
 .. |CondaForge|    image:: https://anaconda.org/conda-forge/fipy/badges/installer/conda.svg
 .. _CondaForge:    https://anaconda.org/conda-forge/fipy
+.. _mamba: https://github.com/mamba-org/mamba
 
 
 --------------

examples/phase/polyxtal.py

@@ -13,6 +13,11 @@
 
 We start with a regular 2D Cartesian mesh
 
+>>> import logging
+>>> logging.basicConfig(level=logging.DEBUG, format='%(asctime)s:%(levelname)s:%(message)s')
+
+>>> logging.debug("begin")
+
 >>> from fipy import CellVariable, Variable, ModularVariable, Grid2D, TransientTerm, DiffusionTerm, ImplicitSourceTerm, MatplotlibViewer, Matplotlib2DGridViewer, MultiViewer
 >>> from fipy.tools import numerix
 >>> dx = dy = 0.025
@@ -22,6 +27,8 @@
 ...     nx = ny = 200
 >>> mesh = Grid2D(dx=dx, dy=dy, nx=nx, ny=ny)
 
+>>> logging.debug("Grid2D initialized")
+
 and we'll take fixed timesteps
 
 >>> dt = 5e-4
@@ -41,6 +48,8 @@
 >>> theta = ModularVariable(name=r'$\theta$', mesh=mesh, hasOld=True)
 >>> theta.value = -numerix.pi + 0.0001
 
+>>> logging.debug("CellVariables initialized")
+
 The ``hasOld`` flag causes the storage of the value of variable from the
 previous timestep. This is necessary for solving equations with
 non-linear coefficients or for coupling between PDEs.
@@ -132,6 +141,8 @@
 ...                                 * (1 - phase)
 ...                                 - (2 * s + epsilon**2 * thetaMag) * thetaMag))
 
+>>> logging.debug("Equations initialized")
+
 The governing equation for orientation is given by
 
 .. math::
@@ -188,6 +199,8 @@
 ...     phase[seed] = 1.
 ...     theta[seed] = numerix.pi * (2 * orientation - 1)
 
+>>> logging.debug("Initial condition set")
+
 and quench the entire simulation domain below the melting point
 
 >>> dT.setValue(-0.5)
@@ -312,15 +325,33 @@
 >>> save_interval = 0.002
 >>> save_at = save_interval
 
+# >>> from fipy import solvers
+# >>> if solvers.solver == "scipy":
+# ...     solver = solvers.LinearGMRESSolver()
+# ... else:
+# ...     solver = None
+
+>>> solver = None
+
+>>> theta_solver = thetaEq.getDefaultSolver()
+>>> logging.debug("theta: {} {}".format(theta_solver, theta_solver.preconditioner))
+>>> phase_solver = phaseEq.getDefaultSolver()
+>>> logging.debug("phase: {} {}".format(phase_solver, phase_solver.preconditioner))
+>>> heat_solver = heatEq.getDefaultSolver()
+>>> logging.debug("heat: {} {}".format(heat_solver, heat_solver.preconditioner))
+
 >>> while elapsed < total_time:
 ...     if elapsed > 0.3:
 ...         q.value = 100
 ...     phase.updateOld()
 ...     dT.updateOld()
 ...     theta.updateOld()
-...     thetaEq.solve(theta, dt=dt)
-...     phaseEq.solve(phase, dt=dt)
-...     heatEq.solve(dT, dt=dt)
+...     res_theta = thetaEq.sweep(theta, dt=dt, solver=solver)
+...     logging.debug("elapsed={}, theta residual = {}".format(elapsed, res_theta))
+...     res_phase = phaseEq.sweep(phase, dt=dt, solver=solver)
+...     logging.debug("elapsed={}, phase residual = {}".format(elapsed, res_phase))
+...     res_heat = heatEq.sweep(dT, dt=dt, solver=solver)
+...     logging.debug("elapsed={}, heat residual = {}".format(elapsed, res_heat))
 ...     elapsed += dt
 ...     if __name__ == "__main__" and elapsed >= save_at:
 ...         timer.set_text("t = %.3f" % elapsed)

examples/phase/test.py

@@ -4,19 +4,19 @@
 
 def _suite():
     return _LateImportDocTestSuite(testModuleNames = (
-                                       'impingement.test',
-                                       'missOrientation.test',
+#                                        'impingement.test',
+#                                        'missOrientation.test',
                                    ),
                                    docTestModuleNames = (
-                                       'binary',
-                                       'anisotropyOLD',
-                                       'anisotropy',
-                                       'quaternary',
-                                       'simple',
-                                       'symmetry',
-                                       'binaryCoupled',
+#                                        'binary',
+#                                        'anisotropyOLD',
+#                                        'anisotropy',
+#                                        'quaternary',
+#                                        'simple',
+#                                        'symmetry',
+#                                        'binaryCoupled',
                                        'polyxtal',
-                                       'polyxtalCoupled'
+#                                        'polyxtalCoupled'
                                    ),
                                    base = __name__)